I use a R.A.T. 7 gaming mouse by MadCatz, and on it, it has 2 extra mouse buttons (4 and 5) I keybound these to commonly used abilities like interrupts and other things, and ever since 4.2, when I use these extra mouse buttons, my game doesn't freeze, but all the other abilities become unable to be clicked on (Yes, I am a clicker, sue me :P). I never had this problem prior to patch 4.2, and it only seems to be a problem with nUI, and yes I did disable all other addons and see if it was still bugged, and it wasn't.
Any help would be appreciated!

I seem to have fixed the problem with nUI5 by removing all key bindings, and then applying them again. As for nUI6, when I use the key bindings I get the same problem. Spells/Abilities become click-through, and once that happens, and I log out, I lose my cursor and have to open up the task manager and restart WoW :\ As nUI6 is still in Alpha, I'm not complaining Another problem I noticed with nUI6 is that when I go to the key bindings page, the section for the nUI buttons is missing, and anything I do try to keybind doesn't go through

I spoke too soon. Apparently it's only bugging out in raids. Works fine solo, but I'm starting to think that it has something to do with the Raid Interface, because I also use the mouse buttons for marking up kill-order/CC's.

nUI doesn't actually know that you're in a raid or not.... more to the point, it just shows or hides frames based on whether or not a given unit exists. It is otherwise blissfully unaware of what you're doing.

Now, that said, one thing that could be in play would be unit frame (aka raid) sorting which should not occur in combat. It's the only part of nUI I can think of that's triggered by the existence of a raid. However, if it did fire while in combat, it could be causing taint which would make your secure actions break and look like your key/mouse bindings/buttons were not working.

You can figure that out easily enough. While out of combat, change the '/nui raidsort' option to disable it (none) then do a '/nui rl' to reload. If the causes the mouse problem to go away, then it is the raid sort that's at issue. If not, then we need to look for something else.

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What people don't get is that I am, ultimately, an artist at heart. My brush has two colors, 1 and 0, and my canvas is made of silicon.

Sorry for such a late reply. I was swamped with work, and didn't have much time to play, but after hours upon hours of testing with the mouse, reprogramming it, and doing all kinds of things with it, nothing worked. Then I decided to unplug and plug it back in. It's amazing how the simplest solutions evade some people. Major derp moment on my part :P